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You will typically find here notes and commentaries on the current biological literature. They are intended to document the post-reductionist, post-Darwinian revolution now in the making. The focus at present is on molecular biology — especially gene regulation and genomic studies as they bear on our understanding of organisms and their evolution. But the contextual, interlinked nature of everything going on in the organism means that you can expect occasional wide-ranging excursions in these commentaries.
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|Posted: May 31, 2019||article 42|
Readers may be forgiven if, having been patiently reading the book to this point, they have experienced a growing frustration. This frustration, as I imagine it, might go like this:
“You have talked about the organism’s story as if it were a meaningful narration, full of purposes. You have talked about chromosome organization in the nucleus, the dynamics of the cytoskeleton, and the identity-preserving role of the cell membrane as if they all held some secret of a more-than-physical coordination of events. You have claimed that the context-dependence of biological processes implies a play of governing ideas. And you have celebrated epigenetics as if it represented an activity of the organism as a whole, which can hardly mean anything less than: the organism as a being or entelechy. A more conventional biology restricts itself to tracing the causal relations among physical parts.
“So, enough with your coy suggestion of some beyond-physical, mystical reality! Isn’t it time to acknowledge that you have a huge problem relating all this to the magnificent body of biological knowledge established on strictly materialistic grounds during the past couple of centuries? This knowledge seems to leave no place for the peculiar terms of your presentation.”
And I agree at least this far: it is time to bring to a focus the decisive questions that seem to lie behind everything I have been talking about. To begin with, then, let us quickly recall how certain key questions have so far been most explicitly raised.
|Posted: May 19, 2019||article 41|
We heard in “The Organism’s Story” that living activity has a certain future-oriented (“purposive” or “intentional” or end-directed) character that is missed by causal explanations of the usual physical and chemical sort. This is true whether the end being sought is the perfection of adult form through development, or the taking of a prey animal for food.
An animal’s end-directed activity may, of course, be very far from what we humans know as conscious aiming at a goal. But all such activity nevertheless displays certain common features distinguishing it from inanimate proceedings: it tends to be persistent, so that it is resumed again and again after being blocked; it likewise tends to be adaptable, changing strategy in the face of altered circumstances; and the entire activity ceases once the end is achieved.
This flexible directedness — this interwoven play of diverse ends and means within an overall living unity — is what gives the organism’s life its peculiar sort of multi-threaded, narrative coherence. Life becomes a story. Events occur, not merely from physical necessity, but because they hold significance for an organism whose life is a distinctive pattern of significances.
The idea of narrative coherence, like the related idea of a governing context, is a mystery for all attempts at purely physical explanation. This is why even the explicit acknowledgment of an organism’s striving for life — central as it may be for evolutionary theory — is discouraged whenever biologists are describing organisms themselves. It sounds too much as if one were invoking inner, or soul, qualities rather than material causes — acknowledging a being rather than a thing. And it is true that our physical laws, however combined, nowhere touch the idea of striving.
|Posted: May 7, 2019||article 40|
You and I harbor trillions of “sub-creatures” in our bodies. I am not referring to the microorganisms in our guts, but rather the cells we consider our own — the constituents of our muscles and brains, our livers and bones, our lenses and retinas. Each of these cells, embedded in its supportive environment, sustains a dauntingly complex and unique way of life. If we had first discovered such cells floating singly in a pool of water and had observed them through a microscope, we would have judged them to be distantly related organisms. Phenotypically (that is, in visible form and function) one cell type can differ from another as much as an amoeba differs from a paramecium.
All the cells in the human body have descended from a single cell (zygote) with a single genome. And just as hundreds of different cell types have arisen from that one zygote, so, too, have the multicellular, intricately organized entities we know as lung, heart, eye, kidney, and pancreas, along with all our other organs. Supremely interdependent as these are, each is nevertheless a functioning organic world of altogether distinctive character.
For the past century these facts of development have been thought to present a (largely ignored) problem for the gene-centered view of life. The developmental biologist Frank Lillie, who had directed the prestigious Marine Biological Laboratory at Woods Hole, Massachusetts, and would go on to become president of the National Academy of Sciences, remarked in 1927 on the contrast between “genes which remain the same throughout the life history” of an organism, and a developmental process that “never stands still from germ to old age”. In his view, “those who desire to make genetics the basis of physiology of development will have to explain how an unchanging complex can direct the course of an ordered developmental stream”.
|Posted: May 7, 2019||article 39|
The centrality of living wholes within biology seems beyond argument. These have not been “put together” or built by an external agency. They are never the results of a physical activity that starts with non-wholes. Biology gives us nothing but beings that have never existed except as wholes possesssing the formative powers that enable them to pass through further stages of physical development.
The one-celled zygote is already a functioning whole. It does not gain further cells through the addition of “building blocks” assembled by an engineer or designer, but rather through an internal power of reorganization and subdivision in which the entire organism participates. All the parts are orchestrated in a unified performance that yields new cells, and particular kinds of cells, just where they are needed. The orchestrating power of the whole can hardly be determined by the particular parts it is bringing into being and orchestrating.
Where the physicist may prefer unambiguous, isolated, and well-defined “point” causes, the biologist never has such causes to theorize about. A biological whole is never absolute, and never perfectly definable as distinct from its environment. Further, its actions are always multivalent, like the meaning of a sentence in a profound and complex text. Its activities interpenetrate one another, like the events of a story.
|Posted: May 7, 2019||article 38|
Throughout a good part of the twentieth century, cell biologists battled over the question, “Which exerts greater control over the life of the cell — the cell nucleus or the cytoplasm?” From mid-century onward, however, the badge of imperial authority was, by enthusiastic consensus, awarded to the nucleus, and especially to the genes and DNA within it. “Genes make proteins, and proteins make us” — this has been the governing motto, despite both halves of the statement being false (which will become ever clearer as we proceed).
The question for our own day is, “Why would anyone think — as the majority of biologists still do — that any part of a cell must possess executive control over all the other parts?” We have already caught our first glimpse of the performances in the nucleus (see Chapter 0), and these hardly testify to domination by a single, controlling agent. Now we will broaden our outlook by making a first approach to the rest of the cell — the cytoplasm, along with its organelles and enclosing membrane.
It would be well to remind ourselves before we proceed, however, that, whatever else it may be, an organism is a physical being. Its doings are always in one way or another physical doings. This may seem a strange point to need emphasizing at a time when science is wedded to materialism. And yet, for the better part of the past century problems relating to the material coordination of biological activity were largely ignored while biologists stared, transfixed, into the cell nucleus. If they concentrated hard enough, they could began to hear the siren call of a de-materialized, one-dimensional, informational view of life.
The idea of a genetic code and program proved compelling, even though the program was never found and the supposedly fixed code was continually rewritten by the cell in every phase of its activity. So long as one lay under the spell woven by notions of causally effective information and code, problems of material causation somehow disappeared from view, or seemed unimportant. And so, freed from “mere” material constraint, programmatic Information became rather like the Designer of the intelligent design advocates.
Surely, even if they are not the decisive causes usually imagined, genes do connect in some manner with the features they were thought one-sidedly to explain. But this just as surely means they must connect physically and meaningfully, via movements and transformations of substance testifying to an underlying narrative — not merely logically, through the genetic encoding of an imagined program. And what we saw earlier about the significant movements and gesturings of chromosomes is only the beginning of the story.
|Posted: May 7, 2019||article 37|
Throughout most of the twentieth century, genes were viewed as the “agents” responsible for an organism’s development, activity, and evolution. Their agency was said to lie in their ability to “regulate”, “organize”, “coordinate”, and “control” physiological processes. DNA, the bearer of these genes, became the “Book of Life” — the essential maker of organisms and driver of evolution. And this view remains stubbornly entrenched today, despite many changes in our understanding. A leading behavioral geneticist has recently written a book entitled, Blueprint: How DNA Makes Us Who We Are.
Nevertheless, the idea that genes are the decisive “first causes” of life — and, more generally, that molecules at the “bottom” ultimately explain everything that happens at larger scales — has come in for a great deal of criticism in recent years. This criticism, as we will see, is fully justified. But the issues can be subtle, as is suggested by an apparent paradox. Philosopher of biology Lenny Moss, who wrote the valuable book, What Genes Can’t Do, has remarked:
“Where molecular biology once taught us that life is more about the interplay of molecules than we might have previously imagined, molecular biology is now beginning to reveal the extent to which macromolecules [such as DNA], with their surprisingly flexible and adaptive complex behavior, turn out to be more life-like than we had previously imagined.”
In a similar vein, I myself wrote a decade ago:
Having plunged headlong toward the micro and molecular in their drive to reduce the living to the inanimate, biologists now find unapologetic life staring back at them from every chromatogram, every electron micrograph, every gene expression profile. Things do not become simpler, less organic, less animate. The explanatory task at the bottom is essentially the same as what we faced higher up.
But if all this is true, what are we to make of Harvard geneticist Richard Lewontin’s declaration, itself hardly disputable, that “DNA is a dead molecule, among the most nonreactive, chemically inert molecules in the living world. That is why it can be recovered in good enough shape to determine its sequence from mummies, from mastodons frozen tens of thousands of years ago, and even, under the right circumstances, from twenty-million-year-old fossil plants … DNA has no power to reproduce itself. Rather it is produced out of elementary materials by a complex cellular machinery of proteins. While it is often said that DNA produces proteins, in fact proteins (enzymes) produce DNA … Not only is DNA incapable of making copies of itself, aided or unaided, but it is incapable of ‘making’ anything else”.
Many astute observers have echoed Lewontin’s remarks, and I have never seen anyone question them, including those who remain enamored of the “Book of Life”. So which is it? When we peer at DNA, do we see a dead molecule or the secret of life? As it happens, there is a simple answer: if we are looking at a molecule conceived in the usual way as a bit of mindless, inherently inert stuff, then, according to our own conceptions, we see only dead stuff. But if we observe the molecule as a system of forces and energies capable of participating and being caught up in the creative life of the cell and organism, then we can hardly help recognizing — and perhaps even reverencing — the living performance unfolding before our eyes.
Saying this is one thing; making it both meaningful and profound is quite another — and that is one task of the present book. So let us begin.
|Posted: January 30 2019||article 36|
Organisms are purposive (“teleological”) beings. Nothing could be more obvious. The fact of the matter is so indisputable that even those who don’t believe it really do believe it. Philosopher of biology Robert Arp speaks for biology as a whole when he writes,
Thinkers cannot seem to get around [evolutionary biologist Robert] Trivers’ claim that “even the humblest creature, say, a virus, appears organized to do something; it acts as if it is trying to achieve some purpose”, or [political philosopher Larry] Arnhart’s observation that … “Reproduction, growth, feeding, healing, courtship, parental care for the young — these and many other activities of organisms are goal-directed”.
And yet, despite his acknowledgment that we “cannot get around” this truth, Arp again speaks for almost the entire discipline of biology when he tries, with some delicacy, to take it all back: “with respect to organisms, it is useful to think as if these entities have traits and processes that function in goal-directed ways” (his emphasis). This as if is a long-running cliché, designed to warn us that the organism’s purposive behavior is deceptive — not quite what it seems. The goal-directedness is, in the conventional terminology, merely apparent or illusory. Certainly it must not be seen as having any relation at all to human purposive activity — an odd insistence given how eager so many biologists are to make sure we never forget that the human being is “just another animal”.
[And from the introductory paragraphs of the concluding section:]
The fact of purposive activity — the obvious play of active agency; the coordination of diverse means toward the realization of countless interwoven and relatively stable ends; the undeniable evidence that animals perceive a world, interpreting and responding to perceptions according to their own way of life; and the coherence of all this activity in a governing unity — we can sum this up by saying that every organism is narrating a meaningful life story. This is not something that a rock, say, loosened by ice and tumbling down the steep slope of a mountain ravine, does in anything like the same manner. The pattern of physical events in the organism is raised by its peculiar sort of coherence toward something like a biography whose “logic” unfolds on an entirely different level from the logic of inanimate physical causation. When we tell a story, the narrative threads convey meanings — for example, motives, needs, and intentions — and these are never a matter of mere physical cause and consequence.
So when I speak of the organism’s wise and knowing agency, or its purposive striving, I refer, among other things, to its capacity to weave, out of the resources of its own life, the kind of biological narrative we observe, with its orchestration of physical events in the service of the organism’s own meanings.
|Posted: November 29 2018||article 35|
We in the twenty-first century have inherited a rich and extensive library of descriptive literature about living things, their habitats, and their mutual relations, bequeathed to us over the centuries by dedicated naturalists. Unfortunately, in this age of molecular biology and genetic preoccupation, the community of naturalists — or, at least, academically connected ones — has largely died out. It is a shame that biologists today can easily pass through their schooling and into a pristine laboratory without ever having read descriptions such as the following, let alone having observed and investigated these phenomena for themselves.
The following narratives, culled from various sources, afford only fragmentary glimpses of the larger panorama of life on earth. But they are enough to remind us of the “miracle” that life can so easily appear to be. The reminder is a useful one, so far as it spurs us toward efforts of understanding that are not cramped by prevailing dogmas.
|Posted: July 12, 2018||article 34|
Every organism is continually dying in order to live. Breaking-down activities are prerequisites for building up. Complex molecules are synthesized, only to be degraded later, with their constituents recycled or excreted. In multicellular organisms such as vertebrates, many cells must die so that others may divide, differentiate, and proliferate.
You and I have distinct fingers and toes thanks to massive cell death during development. The early embryo’s paddle-like hands give way to the more mature form as cells die and the spaces between our digits are “hollowed out”. In general, our various organs are sculpted through cell death as well as cell growth and multiplication. During development the body produces far more neurons than the adult will possess, and an estimated ninety-five percent of the cell population of the thymus gland dies off by the time the mature gland is formed.
Despite all this life and death, I doubt whether anyone would be tempted to describe the embryo’s cells as “red in tooth and claw”. Nor do I think anyone would appeal to “survival of the fittest” or natural selection as the fundamental principle governing what goes on during normal development. The life and death of cells appears to be governed, rather, by the developing form of the whole in which they participate.
But this has been a truth hard for biologists to assimilate, since it has no explanation in the usual causal sense. One way to register the problem is to ask yourself what you would think if I suggested that organisms in populations thrive or die off in a manner governed by the evolutionary outcome toward which they are headed — that the pattern of thriving and dying off, in other words, becomes what it is in order to achieve that outcome. It is not a thought any evolutionist is likely to tolerate. But perhaps the occasional intrepid biologist will be moved to inquire: “Why not? After all, we can also ask about the cells populating our bodies: do they thrive or die off in a manner governed by the forthcoming adult form? And here the answer appears to be a self-evident ‘yes’”.
|Posted: May 15 2018||article 33|
The celebrated physicist Richard Feynman, skeptical of religious or mythic creation stories that focus upon humans and the meaning of their lives, once explained his doubt with arresting simplicity: “The stage is too big for the drama”.
It was a wonderfully succinct way to make his point, and suggests that Feynman had a bit of the poet in him.
The improbably large stage, which he found unsuited to our parochial origin myths, is, of course, the boundless frontier explored by cosmologists, whose probing, high-tech sensors have mapped inter-galactic dimensions of space and time so far beyond our immediate experience that we humans can scarcely hope to comprehend them.
We have all heard many times about our own nondescript place upon this vast stage. We are situated in an unremarkable galaxy among billions of others. Our solar system occupies a scarcely noticeable patch of real estate well out into this galaxy’s hinterlands. And, following the Copernican revolution, we earthlings lost even the circling attention of our neighboring sun and planets.
Still, we reigned unchallenged on our own planet, where we imagined ourselves the possessors of a special destiny, above all other creatures. But then, as a final insult, Darwin re-told our local creation story as a wearyingly long series of accidents, after which we found ourselves to be “trousered apes”.
Oh, the ignominy of it! Or, at least, that seems the usual point of the story. And, to be sure, it stings. The entire account can feel like a soul-crushing blow, rendering coarse or absurd all our higher aspirations, our ideals, our loves. …
|Posted: December 2017||article 32|
Not long ago an intelligent design advocate responded to one of my occasional swipes at ID theory. Thinking I had misinterpreted the theory, he said it was wrong to imagine the Designer working only in the remote past. “ID is open as to when the Designer implements Design”.
My response was along these lines:
For me, the issue isn’t whether a designer acted millions of years ago or a millionth of a second ago. Rather, it’s that the picture being offered is one of a designer working from outside upon a mechanical artifact. But organisms are not machine-like. Their activity is not an outcome of parts assembled by a designing engineer. They are not contrivances periodically requiring service by an outside agent for the sake of evolutionary progress. No, their very life consists of the activity through which they grow and transform their own physical means of acting.
Given today’s charged environment, you might wonder why I did not accuse my correspondent of being a “science-denier.” There is good reason. The label is a dastardly one, poisoning the spirit of evidence-based conversation, which is so crucial to science. It strongly suggests an inquisitorial demand for creedal belief rather than understanding. It almost inspires sympathy for intelligent design theory — and does inspire it for a number of the theory’s proponents, who can be fully as qualified as their authoritarian persecutors, and sometimes far more critically alert.
Some of those who labor to guarantee the purity of evolutionary orthodoxy habitually refer to intelligent design theorists as “IDiots” — and their argumentation naturally tends toward the same exalted level of discourse. To the shame of science, relatively few biologists have yet been willing to call out such behavior. It has mostly been outsiders who have urged greater scientific integrity. For example, the widely respected New York University philosopher, Thomas Nagel, has labeled the biological community’s treatment of intelligent design proponents “manifestly unfair” — this at considerable risk to his own reputation.
History teaches us that the kind of knee-jerk nastiness and vitriol leveled at ID theorists is not uncommon among competing sects trying to differentiate themselves from each other on fine points of sectarian doctrine — nuances that can assume gigantic importance in the minds of the disputants. You have to fight hardest with those who try to occupy your own ground.
That mainstream biologists are quarreling with ID theorists over common ground may seem a strange idea. But look again at the quoted paragraph above. As we will see more clearly in what follows, it applies without reservation to conventional evolutionary theory as well as ID. Few biologists are reticent about their conviction that organisms are machine-like and have been “tinkered” with throughout evolutionary history by a designer capable of producing intelligent results — all without any intelligent aid from organisms themselves.
The designer they have in mind, of course, is natural selection, which has famously been likened to a blind watchmaker and is almost universally referred to as an agent capable of intelligent activity. Selection shapes the bodies and behaviors of organisms, builds specific features, targets or acts on particular genomic regions, favors or disfavors (or punishes) various traits or behavioral strategies, operates in this way or that, maintains DNA sequences, promotes adaptation of populations to local environments, polices mutations and, in general, causes an endless variety of effects.
Not many biologists, whether ID proponents or otherwise, seem particularly interested in confronting the reality of intelligent agency where we observe it directly — in living beings — as opposed to taking the organism merely as evidence for the real guiding intelligence of their preferred Designer. This indifference toward organisms follows rather naturally when you have conceived them as machines, which always require an external designer. But we will take the alternative path, turning toward the organism’s inherent life.
|Posted: Mar 31, 2017||article 31|
When your dog takes a stick in its mouth, drops it at your feet, and then looks expectantly at you while signaling eagerness to run and retrieve the thrown plaything, you have no difficulty recognizing its intentions. Its behavior is blatantly purposive, even if its “state of mind” — whatever that might mean — is very different from yours and mine.
Similarly, if your cat is “telling” you it wants to go outdoors (cats, unfortunately, are always on the wrong side of the door), or if you have watched a bird building a nest, or an amoeba engulfing a particle of food, or the fish in a still pool darting toward the shelter of an overhanging bank upon your approach — you no doubt accept what you see without great puzzlement. We do not expect such behaviors from rocks, clouds, or volcanoes, but they seem normal for living things.
And so they are. Even the “growth behaviors” of plants and the “chemical behaviors” of the individual cells in our bodies are in some sense intelligent and purposive, wisely directed toward need-fulfilling ends. Purposive — or teleological (end-directed) — activity is no merely adventitious feature of living things. Being “endowed with a purpose or project”, wrote one of the twentieth century’s most influential biochemists, Jacques Monod, is “essential to the very definition of living beings”. And according to Theodosius Dobzhansky, a geneticist and leading architect of the past century’s dominant evolutionary theory, “It would make no sense to talk of the purposiveness or adaptation of stars, mountains, or the laws of physics”, but “adaptedness of living beings is too obvious to be overlooked … Living beings have an internal, or natural, teleology”.
The curious thing, however, is that despite this emphatic recognition of the purposive organism, we find in textbooks of biology virtually no mention of purpose — or of the meaning and value presupposed by purpose. To refer to such “unbiological” realities is, it seems, to stumble into the unsavory company of mystics. Yet we might want to ask: if purposiveness in the life of organisms is as obvious as many in addition to Monod and Dobzhansky have admitted, why should it be impermissible for working biologists to reckon seriously with what everyone seems to know?
It’s a question we will ask. Be aware, however, that in struggling to answer it we may stir up unsettling doubts about the central biological concepts of evolution and natural selection.
|Posted: November 10, 2015||article 29|
Molecular biologists have spent several decades trying to identify how “one thing causing another” explains the organism. It is a simplistic and decontextualized way of looking that ends up in radical falsehood. The study of genes and their expression shows us that the organism is a living, intentional activity coordinating its parts in relation to the needs of the whole. Here I try to provide a glimpse of this whole at the molecular level. It is the fullest summary I can offer of how organisms employ their genes, and is preparation for a shift in my writing from gene regulation as such to a much more explicit consideration of the nature of organisms and their evolution.
|Posted: April 29, 2014||article 28|
In Part 1 and Part 2 of this series I have posed and approached the question: How can we understand our own highest conscious functions in relation to the wisdom we find throughout the living kingdoms? The latter includes everything from the intelligence of the chimpanzee and bacterium to the cells of our own bodies. Here in part 3 I try to offer what perspectives I can by way of an answer, while fully respecting the scientific modesty we must currently bring to the question. It’s a bit of a ride, and includes many highly readable (but brief) descriptions of some of the most amazing demonstrations of animal and plant wisdom you will ever hear about.
|Posted: March 26, 2015||article 27|
I suppose it’s finally become official: epigenetics is for real. Its certificate of reality has been issued by the Roadmap Epigenomics Consortium, which last month went public with a trove of reports in Nature and some of its sister publications. A news item on the Nature website summarized the import of the papers this way:
Almost every cell in the human body has the same DNA sequence. So why is a heart cell different from a brain cell? Cells use their DNA code in different ways, depending on their jobs — just as the orchestra [in an accompanying video presentation] can perform one piece of music in many different ways. The combination of changes in gene expression in a cell is called its epigenome.
The symphony orchestra metaphor has some promise. But, as we will see, it’s use in the Nature article is not particularly apt, if only because the “one piece of music” is not the supposed DNA code, but the organism as a whole.
But you say you’ve never quite figured out what epigenetics is? Well, you’re in excellent company. Many molecular biologists seem a little confused about it, too. But the confusion is also an opportunity, since clarifying epigenetics demands that we undo certain damaging intellectual habits within genetics and biology generally. This article is intended as a modest contribution toward that undoing.
|Posted: January 8, 2015||article 26|
In 2006 two Japanese researchers, S. Yamanaka and K. Takahashi, shook up the medical research world by announcing that they had “reprogrammed” adult mouse skin cells (in particular, fibroblasts) to become induced, pluripotent stem cells. Their method: add to the cultured adult cells just four well-chosen genes that result in the over-expression of four gene-regulatory proteins.
This was a time when the debate over the use of stem cells obtained from human embryos was fierce, so the idea that a stem cell might be created (“induced”) from a normal adult skin cell produced quite a sensation.
Laboratories the world over have been running with this discovery ever since, and there were already significant developments by the time I found myself giving a talk at a conference involving a number of molecular biologists. Not having familiarized myself with the work on induced pluripotency, I did not discuss it in my talk, but I did emphasize what seemed to me a decisively important point: there are no “central controllers” or “master regulators” in the cell.
During the discussion period afterward, a researcher at one of the nation’s major stem cell research laboratories aggressively challenged me by stating flatly: “You’re wrong. There are master regulators in the cell. We prove it every day in our laboratory, where we insert just three or four transcription factors in a differentiated cell and cause it to revert to a pluripotent stem cell”.
At the time I could only vaguely allude to research results that, as I was peripherally aware, were already coming in — and then add, “Wait and watch, and you will see. I have no doubt whatever that your master regulators are an illusion”.
|Posted: December 9, 2014||article 25|
A rapidly swelling literature is testifying to the dependence of human welfare upon the diverse microorganisms — collectively, the microbiome (or microbiota) — we play host to. By common admission, we have hardly begun to figure out how these microorganisms affect us — or, I should perhaps say, how they are part of us. But we know enough to appreciate that we could not live normally and healthily (if we could live at all) without them.
The bacteria and other microorganisms in our gut typically outnumber the cells in our body by a factor of ten to one, and their collective genome is orders of magnitude larger than our “own” genome. Remarkably, “one-third of the metabolites in the blood are coming from gut bacteria”, according to Phillip Hylemon, a microbiologist and immunologist at Virginia Commonwealth University in Richmond. Altogether, our microorganisms “function as another organ, complementing and interacting with human metabolism in ways not fully understood”.
You’ll have a hard time believing how the invisible microbes within us function as part of our own life. And perhaps not so hard a time believing how biologists are tempted immediately to regard particular microorganisms as opportunities for exerting neat control over everything from liver cancer to autism.
|Posted: November 11, 2014||article 24|
In biology, the problem of the morphological “type”, or characteristic form, raises the question, When can different features be declared in some sense “the same”? Are the fin of a whale, the wing of a bird, and the arm of a primate the same limb? And if so, what are we recognizing as the common identity? We can ask similar questions when we consider the succession of bones along the spine of a vertebrate, or the succession of leaves along the stem of a plant. In what sense, if any, can we regard these as transformations of a single form? And what might that single form be?
In this article I attempt to summarize an exploration of these questions by the late philosopher, Ronald Brady. Drawing particularly on Johann Wolfgang von Goethe’s work and focusing especially on a leaf sequence along the stem of a single buttercup, he is led to conclusions of dramatic importance. We cannot extract from the leaves a set of common features that enables us to define, in any biologically significant sense, how these leaves “hold together” as a single form. Nor can we find or invent a static schema that generalizes over all the individual leaves. What we actually discover is a unified transformational movement, or gesture, with the individual forms being “snapshots” derived from the gesture.
The transformational movement, as a single gesture, is revealed not only through the sameness of the individual forms in a developmental series, but also through their characteristic differences. A typical or archetypal movement of this sort must continually change in order to remain itself. Moreover — and however much this goes against current thinking — this movement must be regarded as causal in nature. It is the generative principle through which the individual buttercup leaves gain their “buttercup character”.
Brady’s treatment of form and causation contrasts sharply with both conventional biological thinking and the vitalist tendencies that so naturally infect this thinking. It also contrasts with any imputation to organisms of purpose and design analogized either to human purposes and designs or to mechanical operations.
|Posted: September 9, 2014||article 23|
Nine years ago Richard Conn Henry, an astrophysicist at Johns Hopkins University, published an opinion piece in Nature entitled “The Mental Universe”. He urged the scientific community to repeat Galileo’s achievement in “believing the unbelievable”, and recalled Sir James Jeans’ famous remark that “the Universe begins to look more like a great thought than like a great machine”. We don’t know all that this implies, he continued, “but — the great thing is — it is true. ... The Universe is immaterial — mental and spiritual. Live, and enjoy”.
The most dramatic thing about the article was the lack of drama: it produced no visible controversy. After all, physicists have long been accustomed to receive such assertions peaceably, because the science itself seems tolerant of them.
But suppose Henry had made a narrower and more modest claim — just a small part of what he implied in “The Mental Universe”. Suppose he had written only of “The Mental Cell”. Would the occasion have been equally unremarkable? Most molecular and cellular biologists, I suspect, will readily picture the unseemly consequences likely to follow upon the appearance of words like immaterial, mental, and spiritual in their published papers. It would be as if an unspoken taboo were violated.
|Posted: August 1, 2014||article 22|
Vladimir Solovyov (1853-1900) was a Russian philosopher, theologian, literary critic, and poet. His little book, The Meaning of Love — published in the early 1890s, long before the era of sociobiology — is as trenchant and relevant a counterpoint to that modern discipline as you are likely to find today.
I offer here a straightforward summary of parts of Solovyov’s argument, allowing it to stand on its own despite the limitations of nineteenth-century biological knowledge and despite expressions that are bound to grate on modern ears. Yes, the ideas presented here reflect Solovyov’s peculiar era and culture and may therefore appear oddly provincial and dated. But this can usefully remind us that our own thought-forms are, in at least some respects, equally provincial and dated — and will be experienced as such by others soon enough. Far better if we don’t leave that experience entirely to them. Sometimes the easiest way out of the unconsciously constraining assumptions of one’s own cultural context is to listen as earnestly and sympathetically as possible to the “alien” testimony of an earlier era or foreign culture.
These words by Owen Barfield in the book’s preface may serve as an Abstract:
[Solovyov] opens with a biological survey which easily, and to my mind irresistibly, refutes the age-old assumption … that the teleology of sexual attraction is the preservation of the species by multiplication. On the contrary, it is apparent from the whole tendency of biological evolution that nature’s purpose or goal (or whatever continuity it is that the concept of evolution presupposes) has been the development of more complex and, with that, of more highly individualized and thus more perfect organisms. From the fish to the higher mammals quantity of offspring steadily decreases as subtlety of organic structure increases; reproduction is in inverse proportion to specific quality. On the other hand, the factor of sexual attraction in bringing about reproduction is in direct proportion. On the next or sociological level he has little difficulty in showing that the same is true of the factor of romantic passion in sexual attraction. Both history and literature show that it contributes nothing towards the production of either more or better offspring, and may often, as in the case of Romeo and Juliet, actually frustrate any such production at all.
Why then has nature, or the evolutionary process, taken the trouble to bring about this obtrusively conspicuous ingredient in the make-up of homo sapiens? …
Being, at the level of human individuality, is characterized above all by a relation between whole and part that is different from the everyday one that is familiar to us. We may catch a glimpse of it if we reflect, in some depth, on the true nature of a great work of art. … It is a relation no longer limited by the manacles of space and time, so that interpenetration replaces aggregation; one where the part becomes more specifically and individually a part — and thus [to that extent] an end in itself — precisely as it comes more and more to contain and represent the Whole.
Sex-love is for most human beings their first, if not their only, concrete experience of the possibility of such an interpenetration with other parts, and thus potentially with the Whole.
|Posted: July 3, 2014||article 21|
Almost everything you read in the literature of molecular biology today testifies to the seemingly irresistible yet highly problematic search for clearly defined causes as the essential elements of biological understanding. But the more fundamental elements of understanding are contexts possessed of their own expressive character. Here we look at some typical research reports, each of which bears out this truth in its own way.
Viruses, cytoplasmic DNA, and the web of life
The (molecular) days of our lives
DNA and RNA brought to life
Functional vs. nonfunctional DNA binding
|Posted: June 10, 2014||article 20|
From humans to bacteria, every organism is a cognitive creature, carrying out mind-like functions in every aspect of its life. All biologists know this, even if they are strongly encouraged by the reigning intellectual climate to forget it. You can think of this article simply as my way of helping to keep the truth within sight.
It is essential, however, not to pre-judge the term “mind-like”, whose meaning should become clearer in the following text. Be aware that one might speak of the mind-like aspects of simpler organisms (1) without suggesting that these organisms have minds in anything like the familiar human sense, and (2) while recognizing that the effective wisdom playing through the simplest, one-celled organism far transcends any mental achievements we humans are consciously capable of.
|Posted: May 15, 2014||article 19|
A while back I published a criticism of intelligent design (ID) theory entitled “A Sectarian Quarrel? Intelligent Design and Neo-Darwinism”. This was followed more recently by a brief footnote on the same theme, which in turn led to a response on the “home page” of the ID movement — the Discovery Institute’s “Evolution News and Views” website.
Given the ongoing and seemingly intensifying “culture wars” involving (among others) conventional biologists, ID theorists, and a militant cadre of religiously anti-religious “new atheists”, it seems worthwhile to explore some of the issues while ignoring the usual sound and fury. I have addressed the following directly to the theorists of the ID movement, partly as a response to their response to my criticism, but more centrally as an effort of mutual understanding.
To keep the article at a reasonable length, I have had to assume the reader’s familiarity with the general contours of intelligent design theory. Unfortunately — as I have learned by immersing myself in a good deal of ID literature, both pro and con — the public in general has been one-sidedly subjected to the most shamefully (and often intentionally) distorted talking points on the subject, courtesy of what appears to be a very threatened biological establishment.
As for my own severe questioning of intelligent design offered here, I don’t believe you will find much like it anywhere on the current intellectual landscape.
|Posted: April 24, 2014||article 18|
When someone persistently hallucinates, seeing things that aren’t there, we usually assume a cognitive aberration of some sort, if not a severe mental illness. What, then, to make of those countless biologists who look at organisms and think they are seeing machines? Or who look at organs, cells, organelles, and even molecules, and see machines within machines?
I will leave it for you to judge. However, one thing is certain: an inexcusable mistake has gripped the scientific community for decades, severely perverting biological understanding.
I have previously tried to explain in various places why the analogy between organisms and machines fails utterly. But in reading the biological literature lately, I have found the insistent appeals to machinery so egregious, so viciously destructive of scientific insight, and so contrary to the obvious evidence, that I have myself been driven rather too close to a pathological reaction, or at least to an unhelpful exasperation. And so I have decided to gather my thoughts together in what I hope will be a more concise and effective statement.
A good place to start is with a concrete example. ...
|Posted: March 31, 2014||article 17|
Hox genes, often cited as “controllers” of organismal form, turn out to be dependent for their expression on the various factors that control their spatial form in the nucleus.
In a second paper, metabolism is proposed as a replacement for DNA at the head of important causal chains in the organism.
And a special issue of the journal Cell looks for the unifying threads that make sense of the tidal waves of isolated data available to biologists today. Where can those threads be found, if not in the whole organism, as a unity, and not in any particular parts?
In sum, as the feverish obsession with DNA as First Cause continues to lose its force, we may be seeing a long-delayed effort to understand the whole organism. (However, the language of researchers continues to reflect the search for “controlling” elements.)
|Posted: February 11, 2014||article 16|
A molecular web of life
Protein-coding RNAs (messenger RNAs) have been discovered in large communities of mutual regulation. The result of their intricate interplay is an adjustment of gene and protein expression so complex, so fluid, and so continually varying in its details as to blur the distinction between regulators and objects of regulation — and pose insuperable challenges for analysis.
From static to dynamic understanding
A key question is this: when vast numbers of molecules are participating in extended, highly articulated, and directional cellular processes such as cell division or RNA splicing, what keeps them “on-script” when there are a thousand other things they might do — and will do in different contexts? This question is underappreciated due to a lack of imagination in picturing what we already know about how every specific molecular process adapts to the fluid, ever-changing conditions within the organism.
Explaining from the whole to the part
If we are faithful to observation, we recognize that in the organism the larger pattern, or context, should, in the proper sense, be seen as the cause of the the part-processes through which the pattern comes to manifestation. This is the stumbling block for conventional scientists of a materialistic bent. Yet it turns out to be a truth that they implicitly accept and work with all the time.
Courage to name the unknown
Sometimes the prerequisite for scientific advance is courage to put a name to the clearly indicated borders of an unknown territory — a territory we know is there and to which we can assign a definite place in the larger scientific scheme of things, but whose nature and characteristic mode of functioning we do not yet understand. The forming agency so obviously at work in the organism is one such “nameable unknown”.
|Posted: January 16, 2014||article 15|
This article ranges widely in a way that will doubtless surprise you. Some random excerpts:
[Regarding the organization of cells in a hair follicle:] Dramatically, the authors show that “niche stem cells can be dispensable for tissue regeneration, provided that the overall integrity of the niche is maintained”. When the stem cell population in the bulge or hair germ is destroyed by laser ablation, distant epithelial cells flow toward the damaged compartment and go through a transformation of identity enabling them to replace the lost cells. As the authors summarize it, “The overall structure and function of the tissue is maintained because cells are capable of adopting new fates as dictated by their new niche microenvironment”.
It is impossible to reconcile these goings-on in the hair follicle with the picture of an organism being constructed from an available collection of well-defined parts as building blocks. The larger context helps to “decide” what sorts of elements it will have, how they should be transformed, and how they will come into mutual relationship. Nothing could be further from the common picture of the organism or the cell as a product of bottom-up causation, where the sole basis for understanding consists of putting back together in our minds the parts we have previously analyzed out of — and severed from — their life-receiving connection to the whole.
. . . .
When biologists speak of the organism’s activity, who exactly do they mean to say is performing that activity? When they acknowledge that something in the organism is context-dependent, what in fact is it dependent upon — what agency, or unified sphere of activity, or principle, or lawfulness, or other reality of any sort are they appealing to? They cannot be pointing merely to a particular collection of objects, because the collection can be endlessly varied or perturbed, and yet the context remains more or less coherent, and the organism more or less maintains its character. What is coherent? What has this character?
. . . .
I have been emphasizing that the organism is a becoming. This fact makes a lie of the overly emphatic conviction that we learn who we are through a study of evolution. Evolution tells us a great deal — but only about our past. It doesn’t tell us about the potentials of our becoming in the present. When we learn that such-and-such a trait of lower animals is recognizable in ourselves in some form, this knowledge immediately changes our relation to that trait. It opens up a space of freedom to do work and act consciously where previously, rather as with those monarch butterflies migrating south, nature was simply acting through us. “The truth will make you free”. Those who delight in pointing out our “lower nature” are actually assisting us — presumably to their great disappointment, should they become aware of it — toward the realization of a higher nature.
|Posted: December 5, 2013||article 14|
Organisms do things; rocks have things done to them. Even at rest a cat is doing something; rocks do not rest, but are brought to rest. An organism is always engaged in tasks, always going somewhere. Its activity is directed and in some sense intentional and purposeful (“teleological”). Its judgments in responding appropriately to environmental challenges reflect a profound biological wisdom.
From the molecular level on up, organisms mobilize their resources in order to achieve things, whether replicating DNA, splicing RNA, orchestrating cell division, forming embryonic organs, healing wounds, breathing, constructing a nest, securing food, caring for offspring, shedding a skin, maintaining body temperature, hibernating, or anything else we can properly regard as biological activity. Such activity is always part of a life story, and the protagonist in that story is in some sense what every story protagonist must be: a reasoning agent.
This reasoning agent is one of the many wildly diverse creatures on earth whose appearance and ways may strain our credulity and challenge our imagination. Yet, however bizarre its metamorphosing appearance and life cycle may appear to us, its complex and fine-tuned qualitative intelligence is unerring, enabling it to hold itself together and “stay in character” throughout its life and development, even as it differentiates itself internally into a community of organs and tissues that may be as wildly diverse as any external ecological community.
But you will already have asked, quite rightly, what is meant by “reasoning agent”? And even if we are driven to use such a phrase, how can we distinguish an aphid’s “reasoning” from that of a nuclear physicist? This is the question I will address here. Until we sort the matter out, the language of the preceding paragraphs (and of the paragraphs immediately following — and even much of the standard biological literature) invites horrible misunderstandings. Note that I have already twice said, in some sense. We must be on our guard.
|Posted: November 14, 2013||article 13|
It’s become increasingly clear in recent years, that, quite apart from its organelles and cytoskeleton, the cytoplasm is elaborately and “invisibly” organized. Various macromolecular complexes, in more or less defined mixes, congregate in specific locations and sustain a collective identity, despite being unbounded by any sort of membrane. Here we’re looking at structure without even a pretense of mechanically rigid form. How do cells manage that?
A couple of years ago a research duo from the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, and the Department of Chemical and Biological Engineering at Princeton University, writing for the journal, Developmental Cell, framed the problem this way:
“Non-membrane-bound macromolecular assemblies found throughout the cytoplasm [inner contents of the cell] and nucleoplasm [contents of the nucleus] … consist of large numbers of interacting macromolecular complexes and act as reaction centers or storage compartments. ... We have little idea how these compartments are organized. What are the rules that ensure that defined sets of proteins cluster in the same place in the cytoplasm? (Hyman and Brangwynne 2011)
Even more puzzling, a “compartment” can maintain its identity despite the rapid exchange of its contents with the surrounding cytoplasm. “Fast turnover rates of complexes in compartments can be found throughout the cell. How do these remain as coherent structures of defined size and shape when their components completely turn over so quickly?”
[Read More (Note: the above excerpt is not at the article’s beginning).]
|Posted: October 24, 2013||article 12|
This article is a brief introduction and commentary relating to a new paper appearing on the “Biology Worthy of Life” website: “Look What’s Happened to Genetic Synonyms!”
Following immediately upon the discovery of the double helical structure of DNA in 1953, some of the most brilliant scientists from several disciplines pooled their efforts in a feverish quest to lay bare the secret of the “genetic code”. Their invigorating struggle lasted about a decade, and ever since then, the code has lain at the foundation of biological understanding — and misunderstanding.
The aim of the decoding effort was to learn how the “letters” of a DNA sequence mapped to the amino acid sequence of the cognate protein. As it turned out, the solution was rather disappointing, as most scientists saw it. Having anticipated the most elegant bit of computer-like programming imaginable, they found a genetic code they could only term “redundant” or “degenerate” because of its apparent inefficiency. It was as if the dots and dashes of the Morse code mapped to the English alphabet, not one-to-one, but rather with individual English letters corresponding to several different dot-dash patterns.
|Posted: September 29, 2013||article 11|
One of the unquestioned certainties of the human genome has long been that nearly all cells in our bodies contain identical DNA. (Some cancerous tissues and certain immune cells are major known exceptions.) Another truth has seemed so evident as to require little explicit statement: DNA knows its proper place in the cell, and stays there. Yet on both counts the reigning convictions have turned out to be more than a little shaky. And on both counts the emerging evidence testifies to yet more things the organism does to manage its own genome.
In a previous posting I reported on our “genetically mosaic” bodies, describing how different groups of cells or tissues in the same body possess somewhat different genomes. This, of course, contravenes a long-running assumption about the overall genetic uniformity of the organism. There was supposed to be just one “plan” (or “recipe” or “Book of Life”), not many variants of it. If there are different versions of the plan, then either biologists will be sent on a fruitless search for a distinct “master plan” that “controls” the relations between the subordinate plans, or (one rather hopes) they will begin to give more credence to the agency of the organism itself as a living whole — the organism they already incessantly speak of as a thoughtful agent.
Here I will add something about the refusal of DNA to stay where it “belongs”. Indeed, the remarkable thing is that DNA, so often viewed as an endpoint of cell signaling, has now been found to look suspiciously like a signaling molecule itself. Or, at least, fragments of it do. ...
|Posted: September 12, 2013||article 10|
I’ve just finished reading Darwin’s Doubt, a newly released critique of mainstream (neo-Darwinian) evolutionary theory and a defense of intelligent design. The author is Stephen Meyer of Seattle’s Discovery Institute, an organization often considered to be the chief incubator of the intelligent design movement.
Here I offer no summary or review of the book, but only a single and (so I believe) decisive line of thought. I should say first, however, that, as an assessment of the challenges facing evolutionary theorists on several fronts today, the book seems to me at least as creditable as many productions by contemporary neo-Darwinian biologists. And, in his attempt to convince the reader through calm argument, the author rises above the shrill, apparently frightened, and scarcely scientific rhetoric we’ve been hearing for years from some of the more militant, self-identified atheists and anti-intelligent design types.
As most long-time readers will have recognized, I am no more an intelligent design type myself than I am a conventional Darwinian thinker. And in fact my aim now is to characterize the common ground upon which those two camps have taken up arms, and to suggest that they might achieve a healthy détente by simply abandoning their unproductive field of battle and turning toward the organism itself. ...
|Posted: August 22, 2013||article 9|
In 1992 the preeminent geneticist, Walter Gilbert, memorably dramatized the significance of the Human Genome Project by telling audiences how in the future every individual’s genomic sequence will be inscribed on a digital disk. He then illustrated this future by pulling a CD out of his pocket, holding it up, and saying, “Here is a human being; it’s me”.
It now appears likely, however, that when such a future comes he will need to carry around many disks, each containing a unique digital sequence corresponding to one of the multiple genomes in his own body. His problem will then be to decide which disk holds the real Walter Gilbert. ...
|Posted: August 2, 2013||article 8|
A dose of ionizing radiation equal to 10 grays (a measure of absorbed radiation) is lethal to the human body. Most bacteria cannot survive 200 grays. But then there is the bacterium known as Deinococcus radiodurans: it can endure over 17,000 grays and do quite well, thank you. Never mind that its genome is thoroughly shattered by the assault.
Here’s what happens. Ionizing radiation can damage DNA in various ways, perhaps worst of all by causing double-strand breaks. These are breaks across both strands of the DNA double helix. The familiar bacterium, E. coli, not at all untypically, dies when it suffers about four double-strand breaks per each of its four-to-eight circular DNA molecules. Deinococcus radiodurans, by contrast, can survive over a thousand double-strand breaks. This means that it continues life after its genome is broken into hundreds of small fragments. It does so by proceeding to put its genome back together again when living conditions improve — a daunting task, to say the least. ...
|Posted: July 19, 2013||article 7|
On the Biology Worthy of Life website I have posted a new document entitled, “How the Organism Decides What to Make of Its Genes". It is perhaps the strangest piece I have ever published, being the only one I would advise you not to try to read. It is also the only one almost guaranteed in advance to contain at least some bits of misleading information. And, most importantly, it may be the one most likely to seriously mess with the heads of practicing biologists, many of whom (I have slowly come to recognize) are so burdened by the demands of their narrow fields of research that they may scarcely be aware of much of the literature even in disciplines rather closely related to their own. The document in question is intended to provide the kind of healthy shock that may come from suddenly gaining a much wider vantage point. ...
Pervasive Transcription: Using Genomes “Every Which Way” (article 6, July 4, 2013)
Are “Disordered” Proteins Really Disordered? (article 5, June 25, 2013)
What Absent Genes Don’t Do — And How Can We Know? (article 4, June 15, 2013)
The Paradox in “Explaining” Form (article 3, June 15, 2013)
The Complex Performance of the Three-Dimensional Chromosome (article 2, June 10, 2013)
Signals and the Whole Organism (article 1, June 7, 2013)
This document: RediscoveringLife.org
Steve Talbott :: Rediscovering Life